Download all models

Additional information

Those automatically generated models are only partially parameterized. In the case of KEGG signaling pathways for which no mechanistic details are provided, the models (with qual constructs) contain only topological relationships together with interaction signs. No logical rules specify the effects of (combined) interactions, and these models should be seen as scaffolds to be further parameterized before use in simulation. This can be done either by considering default, yet biologically meaningful, logical functions (e.g., requiring the presence of at least one activator and absence of all inhibitors) [Nobeli2003], by doing further manual refinement of the model (e.g., by literature mining), or by using dedicated experimental data to identify the functions [MacNamara2012].

Several simulation tools now support the SBML Level 3 qual package, including GINsim, CellNOpt and The Cell Collective platform. CellNOpt provides a pipeline to generate logical rules by pruning a general scaffold with all possible rules so as to find the submodel that best describes the data. This can be done using various formalisms [Terfve2012] of increasing detail, depending of the data at hand. The Cell Collective platform includes Bio-Logic Builder to facilitate the conversion of biological knowledge into a computational model [Helikar2012]. GINsim provides complementary features that allow performing multiple analyses of logical models using powerful algorithms [Chaouiya2012]. Therefore, relying on a combined use of these tools, one could use the Path2Models qualitative models by training them against data of, for instance, a cell type of interest, and subsequently analyzing the resulting models.

References

For more information about the initial effort behind this branch, please refer to the Google project page of path2models. This project has now been completed. Models generated from other efforts are been added to this branch.